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Journal Articles Plant Journal Year : 2018

The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution

Kristian Ullrich
  • Function : Author
Jörg Fuchs
  • Function : Author
Fabian Haas
Carl Li
  • Function : Author
Guillaume Blanc
Michiel van Bel
Rabea Meyberg
Jordi Morata
  • Function : Author
Manuel Hiss
  • Function : Author
Wellington Muchero
  • Function : Author
Lee Kamisugi
  • Function : Author
Eva Decker
  • Function : Author
Nico van Gessel
  • Function : Author
Sean Graham
  • Function : Author
Lee Gunter
  • Function : Author
Daniel Mcdaniel
  • Function : Author
Sebastian N.W. Hoernstein
  • Function : Author
Fay-Wei Li
Pierre-François Perroud
Jeremy Phillips
  • Function : Author
Daniel Rokshar
  • Function : Author
Carl Rothfels
Lucas Schneider
  • Function : Author
Shengqiang Shu
  • Function : Author
Dennis Stevenson
  • Function : Author
Fritz Thümmler
  • Function : Author
Michael Tillich
  • Function : Author
Juan Villarreal Aguilar
  • Function : Author
Thomas Widiez
Ann Wymore
  • Function : Author
Yong Zhang
  • Function : Author
  • PersonId : 946448
Ralph Quatrano
  • Function : Author
Klaus F.X. Mayer
  • Function : Author
Josep Casacuberta
Klaas Vandepoele
Andrew Cuming
  • Function : Author
Florian Maumus
Stefan Rensing

Abstract

The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene- and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.

Dates and versions

hal-01760352 , version 1 (06-04-2018)

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Daniel Lang, Kristian Ullrich, Florent Murat, Jörg Fuchs, Jerry Jenkins, et al.. The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution. Plant Journal, 2018, 93 (3), pp.515 - 533. ⟨10.1111/tpj.13801⟩. ⟨hal-01760352⟩
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